Abstract Aim By establishing a prehistoric fossil record for the vertebrate fauna of Guam, we can document the composition of the island’s fauna prior to Western contact. It will also complement the extensive prehistoric fossil data already known from the nearby islands of Rota, Tinian and Aguiguan, and improve our understanding of natural distributional patterns through a chronologically deeper view of the biogeography of the Mariana Islands. Location Northern Guam, Mariana Islands, Micronesia. Methods Fossil-bearing sediment was removed from karst features with vertically and horizontally controlled excavation methods. Age determinations of the fossils were estimated by radiocarbon dating associated wood charcoal samples. Results The 3314 bones (fossils) of terrestrial vertebrates date to the past two millennia and represent 34 species. Among 12 species of squamate reptiles, one is extinct (a gekkonid lizard) and another, the monitor lizard, Varanus indicus, was introduced to Guam no later than about 1600 years ago. The 17 species of birds feature five that are extinct. Two others not recorded previously on Guam are extirpated. Eight others were lost on Guam in historic times. We also recovered bones of two species of indigenous bats, (Pteropus sp., extirpated; Emballonura semicaudata, probably extirpated), and non-native rodents, (Rattus spp.). Main conclusions Guam’s contemporary faunal losses have been well documented since invasion of the Brown Treesnake (Boiga irregularis) during or shortly after WWII. Other exotics, as well as habitat deterioration, have abetted this snake’s deleterious presence. Our data further show that human impact led to declines or losses of vertebrate populations by late prehistoric times. Numerous anthropogenic extirpations would not be evident without studying fossils. Our chrono-stratigraphic evidence argues for the arrival of non-native rats (Rattus sp.) only about 1000 years ago, which helps to explain why a flightless rail survived on Guam into modern times, unlike on most other islands in Oceania.